[2024-01-24 13:17:59,307] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:59,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:59,309] [INFO] DQC Reference Directory: /var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference
[2024-01-24 13:18:00,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,643] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,644] [INFO] Running command: gunzip -c /var/lib/cwl/stga4e31f9a-011f-4787-992d-291b85aa04e6/GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/cds.fna -a GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:07,690] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:07,691] [INFO] Task started: HMMsearch
[2024-01-24 13:18:07,691] [INFO] Running command: hmmsearch --tblout GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference/reference_markers.hmm GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:07,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:07,961] [INFO] Found 6/6 markers.
[2024-01-24 13:18:07,989] [INFO] Query marker FASTA was written to GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:18:07,990] [INFO] Task started: Blastn
[2024-01-24 13:18:07,990] [INFO] Running command: blastn -query GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference/reference_markers.fasta -out GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,724] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:08,724] [INFO] Target genome list was writen to GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:18:08,734] [INFO] Task started: fastANI
[2024-01-24 13:18:08,734] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e31f9a-011f-4787-992d-291b85aa04e6/GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna.gz --refList GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:16,946] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:16,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:16,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:16,960] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:16,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:16,960] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acinetobacter albensis	strain=ANC 4874	GCA_900095025.1	1673609	1673609	type	True	100.0	999	1000	95	conclusive
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	82.9785	716	1000	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	82.278	619	1000	95	below_threshold
Acinetobacter terrestris	strain=ANC 4471	GCA_004331155.1	2529843	2529843	suspected-type	True	81.9628	623	1000	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	80.9081	563	1000	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.0905	490	1000	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	79.6633	424	1000	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.595	388	1000	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	79.4837	421	1000	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.0371	358	1000	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.6902	339	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:16,962] [INFO] DFAST Taxonomy check result was written to GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:18:16,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:16,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:16,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference/checkm_data
[2024-01-24 13:18:16,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:16,994] [INFO] Task started: CheckM
[2024-01-24 13:18:16,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/checkm_input GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:18:44,963] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:44,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,980] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:44,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:44,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:18:44,982] [INFO] Task started: Blastn
[2024-01-24 13:18:44,982] [INFO] Running command: blastn -query GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge7edb07f-7bae-47d0-b9fa-3825c80f9088/dqc_reference/reference_markers_gtdb.fasta -out GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:46,136] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:46,139] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:46,139] [INFO] Target genome list was writen to GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:46,147] [INFO] Task started: fastANI
[2024-01-24 13:18:46,148] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e31f9a-011f-4787-992d-291b85aa04e6/GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna.gz --refList GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:54,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:54,046] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:54,046] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900095025.1	s__Acinetobacter albensis	100.0	999	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.07	97.99	0.85	0.82	4	conclusive
GCF_000367925.1	s__Acinetobacter bohemicus	82.9764	715	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_002135335.1	s__Acinetobacter sp002135335	82.7471	675	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107285.1	s__Acinetobacter kyonggiensis	82.6778	701	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCF_013004375.1	s__Acinetobacter terrae	82.2908	618	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_004331285.1	s__Acinetobacter sp004331285	82.2249	658	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336635.1	s__Acinetobacter sp004336635	82.1764	623	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_001647545.1	s__Acinetobacter sp001647545	81.9797	665	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.85	96.85	0.89	0.89	2	-
GCF_004331155.1	s__Acinetobacter terrestris	81.9748	622	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	-
GCF_002135315.1	s__Acinetobacter sp002135315	81.1697	583	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816495.1	s__Acinetobacter harbinensis	80.9081	563	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:54,048] [INFO] GTDB search result was written to GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:54,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:54,051] [INFO] DFAST_QC result json was written to GCF_900095025.1_IMG-taxon_2671180230_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:18:54,051] [INFO] DFAST_QC completed!
[2024-01-24 13:18:54,051] [INFO] Total running time: 0h0m55s